Contributions
Abstract: EP325
Type: E-Poster Presentation
Session title: Acute lymphoblastic leukemia - Biology & Translational Research
Background
Acute lymphoblastic leukemia (ALL) is the most prevalent type of pediatric cancer. Even though, 85-90% of patients with ALL can reach a long-term cure, ALL does reoccur in about 15-20% of all patients and can be cured in just 30-50% of the relapsed cases. ALL is molecularly characterized by an increasing number of structural genomic aberrations that strongly correlates with prognostic and clinical outcomes. Usually, a combination of cyto- and molecular genetic methods (karyotyping, array-CGH, FISH, RT-PCR, RNA-seq) is needed to identify all the underlying genomic aberrations present in ALL.
Aims
This research aims to investigate the feasibility of next-generation cytogenomics to detect structural variants in an all-in-one approach.
Methods
As proof of principle, twelve pediatric B-cell precursor ALL samples from ALL-BFM-2000 and AIEOP-BFM-ALL-2017 were analyzed by means of optical genome mapping (OGM), a DNA-based approach for structural variant detection, using the Saphyr system (Bionano Genomics). Intensive validation of the results was performed by comparing OGM data to existing data from routine diagnostic workflows.
Results
All structural alterations among translocations (e.g., t(1;19), dic(9;12)), aneuploidies (e.g., -7, -11, high hyperdiploidy), and copy number variations (e.g., IKZF1plus profile) detected by established techniques were identified by OGM as well. Additionally, OGM revealed a more complex structure of a known translocation t(12;21) and detected further alterations, among those a small deletion in SETD2 as well as a stratification relevant gene fusion of JAK2/NPAT in an archived sample.
Conclusion
In this pilot study of very well characterized pediatric ALL cases we show that all previously known genomic aberrations were detected by means of OGM as well and that OGM has the potential to detect stratification-relevant markers in an all-in-one approach.
Keyword(s): Acute lymphoblastic leukemia, Fusion, Molecular cytogenetics, Risk factor
Abstract: EP325
Type: E-Poster Presentation
Session title: Acute lymphoblastic leukemia - Biology & Translational Research
Background
Acute lymphoblastic leukemia (ALL) is the most prevalent type of pediatric cancer. Even though, 85-90% of patients with ALL can reach a long-term cure, ALL does reoccur in about 15-20% of all patients and can be cured in just 30-50% of the relapsed cases. ALL is molecularly characterized by an increasing number of structural genomic aberrations that strongly correlates with prognostic and clinical outcomes. Usually, a combination of cyto- and molecular genetic methods (karyotyping, array-CGH, FISH, RT-PCR, RNA-seq) is needed to identify all the underlying genomic aberrations present in ALL.
Aims
This research aims to investigate the feasibility of next-generation cytogenomics to detect structural variants in an all-in-one approach.
Methods
As proof of principle, twelve pediatric B-cell precursor ALL samples from ALL-BFM-2000 and AIEOP-BFM-ALL-2017 were analyzed by means of optical genome mapping (OGM), a DNA-based approach for structural variant detection, using the Saphyr system (Bionano Genomics). Intensive validation of the results was performed by comparing OGM data to existing data from routine diagnostic workflows.
Results
All structural alterations among translocations (e.g., t(1;19), dic(9;12)), aneuploidies (e.g., -7, -11, high hyperdiploidy), and copy number variations (e.g., IKZF1plus profile) detected by established techniques were identified by OGM as well. Additionally, OGM revealed a more complex structure of a known translocation t(12;21) and detected further alterations, among those a small deletion in SETD2 as well as a stratification relevant gene fusion of JAK2/NPAT in an archived sample.
Conclusion
In this pilot study of very well characterized pediatric ALL cases we show that all previously known genomic aberrations were detected by means of OGM as well and that OGM has the potential to detect stratification-relevant markers in an all-in-one approach.
Keyword(s): Acute lymphoblastic leukemia, Fusion, Molecular cytogenetics, Risk factor